3.Application and evaluation of droplet digital polymerase chain reaction in detection of severe acute respiratory syndrome corona virus-2
CHEN Shuang ; WANG Ming-yue ; ZU Zhen ; TANG Yun ; YE Sheng ; LING Hua ; TAN Zhang-ping
China Tropical Medicine 2023;23(5):495-
Abstract: Objective To analyze the nucleic acid detection results of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) by droplet digital PCR (ddPCR) and compare with the detection results of real-time fluorescence quantitative RT-PCR (qRT-PCR), so as to evaluate the advantages and disadvantages of detection, and to provide data support for optimizing the nucleic acid detection scheme of SARS-CoV-2. Methods According to the SARS-CoV-2 specific primer probe published by the China Center for Disease Control and Prevention, a ddPCR detection method for SARS-CoV-2 was designed. One sample was selected for sensitivity test after gradient dilution; six respiratory virus nucleic acid positive samples including seasonal H3N2 influenza virus and SARS-CoV-2 positive samples were selected for specificity test; five SARS-CoV-2 positive samples were selected for repeatability test; in addition, 30 positive and 20 negative SARS-CoV-2 samples were selected for multiple clinical samples testing, and the results were analyzed and compared with those of qRT-PCR. Results The ddPCR method can specifically detect SARS-CoV-2, and directly obtain the original copy number of the sample target gene to achieve accurate quantification; the sensitivity test of gradient dilution positive samples showed that qRT-PCR detected target genes in part of the 10-5 dilution of samples, and no target genes were detected in 10-6 dilution, while ddPCR detected all target genes in both 10-5 and 10-6 dilution of samples. The detection limit of ddPCR was two orders of magnitude higher than that of qRT-PCR, and the sensitivity was higher than that of qRT-PCR; in the comparison of the repeatability test results of the two methods, the coefficient of variation of ddPCR was 1.266%-11.814%, lower than 1.729%-26.174% of qRT PCR, and the repeatability was higher than qRT-PCR; among 50 clinical samples, 30 positive samples of confirmed cases of Coronavirus Disease 2019 (COVID-19) were detected by both methods, SARS-CoV-2 was successfully detected by both methods, and 20 negative samples of COVID-19 were detected by both methods, and the results were negative, with a coincidence rate of 100.00% (50/50). Conclusion The ddPCR method can accurately quantify SARS-CoV-2 with strong specificity, and its sensitivity and repeatability are higher than those of qRT-PCR, but it also has certain detection limitations and is more suitable for the detection of low load samples. In the actual detection, the two methods can be reasonably combined to improve the detection accuracy.
4.Epidemiological analysis of plague in Qinghai province between 2000 and 2009
Ke-mei, WU ; Yong-hai, YANG ; Yuan-zhong, WANG ; Xue, WANG ; Zhi-zhen, QI ; Zu-yun, WANG
Chinese Journal of Endemiology 2011;30(4):437-440
Objective To analyze the endemic features of plague in Qinghai province between 2000 and 2009, discover the law of occurrence and progression, in order to provide a scientific basis for further prevention and treatment of the disease. Methods Descriptive epidemiology was employed to analyze the data from on the spot investigation, monitoring reports and papers published between 2000 and 2009. The indicators included the area, host and media distribution of animal plague and area, time, and population distribution of human plague.Results In Qinghai province between 2000 and 2009, 189 strains of Yersinia pestis were isolated from a variety of animals and insect vectors, including 77 from the marmot, accounting for 40.74%, 40 from Callopaylla dolabris,accounting for 21.16%. Positive serum antibodies against F1 plague were detected in 238 samples, including 90 samples from husbandry dogs, 63 from woodchucks. The areas with Yersinia pestis were consistent with the areas with positive serum antibodies against F1 plague, which distributed mainly along the Qinghai-Tibet railway Wulan county, Delhi and Golmud Multi-county;confirmed that there was natural foci of plague in Qinghai vole. Between 2000 and 2009, 13 events of human plague occurred, with 37 cases and 16 patients died, mortality was 43.24%.Cases were distributed in 11 townships of Tongde, Xinghai, Qilian, Wulan, Tianjun, Nangqian, Qumalai,Chengduo and Zhiduo counties. May to October was the disease season, with September the peak. Pneumonic plague disease type was the main mode of transmission of the plague and patients often contacted with airborne droplets through the air and peeling fresh Marmota. Conclusions Plague in Qinghai province is still grim,strengthening animal plague surveillance, and timely disposal of animal plague, improving the province's agricultural and pastoral areas, especially increase the disease prevention consciousness of the masses are future tasks. Work should be focused on strengthening the prevention and control of plague along Qinghai-Tibet railway,and prevent the occurrence and long-distance transmission of human plague.
5.Identification of a new subtype of blaADC produced by Acinetobacter baumannii isolated in children.
Rui-zhen ZHAO ; Qian CHEN ; Yue-jie ZHENG ; Zu-huang MI
Chinese Journal of Epidemiology 2007;28(10):1009-1012
OBJECTIVETo investigate the genotype of blaADC which was a kind of AmpC produced by Acinetobacter baumannii (AB), isolated through the detection of 28 similar strains among children.
METHODS28 strains of AB were collected and isolated from the Pediatrics clinic during 2006, and were identified through bacteria and susceptibility test using Vitex-32 automicroscan GNI and GNS cards. The genotype of blaADC was confirmed by polymerase chain reaction (PCR) and them sequenced.
RESULTS3 of the 28 strains of AB showed multi-drugs resistance, with a positive rate of 10.71%. blaADC was discovered in 17 of the 28 strains and the positive rate was 60.71%. All the 28 strains of AB were resistant to Cefoxitin. blaADC positive strains were all sensitive to Ampicil/Sulbactam, and only one of them was resistant to Piperacillin/Tazobactan. There were no blaADC genes discovered in the strains that were resistant to Ampicil/Sulbactam or Piperacillin/Tazobactan. There were changes of amino acids on the site 4, 242, 342 and 376 in the sequence of blaADC of No.2 strain, comparing to gi /7258342/ emb /CAB77444. 1/ in GenBank.
CONCLUSIONAbove 60% of the AB isolated in children were carrying blaADC while a strain was collected from them at random. When they were undertaken nucleotide sequence analysis, significant difference was found from the others that landed in GenBank, which identified itself as new subtype.
Acinetobacter Infections ; microbiology ; Acinetobacter baumannii ; classification ; drug effects ; genetics ; isolation & purification ; Amino Acid Sequence ; Anti-Bacterial Agents ; pharmacology ; Bacterial Typing Techniques ; Child ; DNA, Bacterial ; genetics ; Drug Resistance, Multiple, Bacterial ; genetics ; Genotype ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; beta-Lactamases ; genetics
6.Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography.
Xiao-long LU ; Qin ZHENG ; Xian-zhen YIN ; Guang-qing XIAO ; Zu-hua LIAO ; Ming YANG ; Ji-wen ZHANG
Acta Pharmaceutica Sinica 2015;50(6):767-774
The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new indicator for the granulating process control and optimization.
Drugs, Chinese Herbal
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analysis
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Fractals
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Medicine, Chinese Traditional
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Powders
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Quantitative Structure-Activity Relationship
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Synchrotrons
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Technology, Pharmaceutical
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Tomography, X-Ray Computed
7.Study on the molecule epidemiological between resistances of 7 genes interrelated 4 antibiotic to isolated Streptococcus pneumoniae in children.
Yun-fang DING ; Zu-huang MI ; Jian-hua ZHANG ; Yun-zhen TAO ; Ling QIN
Chinese Journal of Epidemiology 2005;26(6):435-439
OBJECTIVETo investigate the molecule epidemic for 7 genes interrelated penicillin, erythromycin, tetracycline, vancomycin resistance of isolated Streptococcus pneumoniae (SP) in children at Suzhou area.
METHODS(1) Thirty-one pneumococcal isolates were collected from respiratory tract secretions of children with respiratory diseases from Nov 2002 to Apr 2003 at the Children's Hospital of Suzhou University (reference strain ATCC49619). (2) Penicillin susceptibility was determined by E-test, while erythromycin, tetracycline, vancomycin were determined by K-B disk. (3) The detecting of pbp2B, ermA/B, mefA, tetM, vanA, vanB genes by PCR, Sequencing pbp2B genes, Contrasting pbp2B DNA sequences among pneumococcal isolates and SP R6 [penicillin sensitive (www.ncbi.nlm.gov/nucleotide, NC-003098)].
RESULTSOf thirty-one isolates studied, the results were shown as follows; (1) Penicillin sensibility 38.7% (n = 12), penicillin resistance 61.3% (n = 19), pbp2B mutation 64.5% (n = 20); (2) Erythromycin sensibility 9.7% (n = 3), erythromycin resistance 90.3% (n = 28), ermA/B 71% (n = 22), mefA 32.1% (n = 10), ermA/B + mefA 87.1% (n = 27); (3) Tetracycline sensibility 9.7% (n = 3), tetracycline resistance 90.3% (n = 28), tetM 90.3% (n = 28); (4) Vancomycin sensibility 100% (n = 31), vanA, vanB all 0%.
CONCLUSIONAmong pneumococcal isolates at our area, penicillin, erythromycin, tetracycline resistance were high, vancomycin was sensitive. Detecting 7 genes interrelated penicillin, erythromycin, tetracycline, vancomycin resistance expressed genotypies for antibiotic resistances in pneumococcal isolates.
Anti-Bacterial Agents ; pharmacology ; Child ; China ; epidemiology ; DNA, Bacterial ; genetics ; Drug Resistance, Multiple, Bacterial ; genetics ; Erythromycin ; pharmacology ; Female ; Humans ; Male ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Penicillin Resistance ; genetics ; Pneumococcal Infections ; epidemiology ; microbiology ; Streptococcus pneumoniae ; drug effects ; genetics ; isolation & purification ; Tetracycline Resistance ; genetics ; Vancomycin ; pharmacology
8.Protective effect and mechanism of ginsenoside Rg1 on H2O2induced hippocampal neurons aging due to down-regulate NOX2 mediated NLRP1 inflammasome activation in vitro
Tan-Zhen XU ; Ya-Li CHEN ; Xiao-Yan SHEN ; Ling-Ling SUN ; Bi-Qiong ZHANG ; Da-Ke HUANG ; Wei-Zu LI
Chinese Journal of Pharmacology and Toxicology 2018;32(4):321-321
OBJECTIVE To explore the protective effects and mechanisms of Ginsenoside Rg1 (Rg1) on H2O2-induced hippocampal neurons aging in vitro. METHODS The primary culture hippo-campal neurons(7 d)were randomly placed into six groups:normal control group,H2O2(200 μM)treat-ment group,and H2O2+Rg1(1,5 and 10μM)groups.The neurons were with Rg1(1,5 and 10 μmol·L-1) for 6h. H2O2(200 μmol·L-1) was added to the medium and incubate for 18 h. The Dihydroethidium (DHE) staining was performed for ROS production assessment. The LDH release and Hoechst 33258 were performed to examine the neuronal damage and apoptosis. The immunoblot was used to deter-mine the expression of β-Gal,NOX2,p22phox,p47phox,NLRP-1,ASC and Caspase-1 in hippocampal neurons.The ELISA was performed to detect the levels of IL-1β and IL-18 released in the supernatant in hippocampal neurons.RESULTS Rg1(5 and 10 μmol·L-1)significantly reduced the ROS production, attenuated H2O2-induced neuronal damage and apoptosis (P<0.05, P<0.01). The immunoblot results showed that Rg1(5 and 10 μmol·L-1)treatment significantly decreased the expression of β-Gal,NOX2, p22phox,p47phox,NLRP-1,ASC and Caspase-1 in hippocampal neurons(P<0.05,P<0.01).Additionally, Rg1(5 and 10 μmol·L-1)treatment significantly decreased IL-1β and IL-18 release in the supernatant. CONCLUSION The protective effect of Rg1 in H2O2-induced hippocampal neurons aging may be due to inhibit NOX2-NLRP1 activation.
9.Epidemiologic analysis on human plague of Sanjiangyun Area in Qinghai Province, China
Guo-jun, WANG ; Chao, LI ; Zhi-zhen, QI ; Li, WANG ; Hu, WANG ; Zu-yun, WANG ; Yi, ZHENG ; Bai-zhong, CUI ; Xiang, LI ; Bao-hong, MA
Chinese Journal of Endemiology 2008;27(2):207-209
Objective To study on epidemiologic characteristics of human plague cases in Sanjiangyuan Area,and provide theoretical basis to work out the preventive measures.Methods Based upon the epidemiology information from the human plague case data bank of Qinghai Province,human plague data were analyzed retrospectively in Sanjiangyun Area by sorting,verifying and summing up of these data,including some of case file and monitoring data.Results Except for 12 years in the period of 1960 to 2006,there were human plague cases happened every year.The morbidity occurred mainly in 12 counties of 4 states,including Yushu,Guolou,Huangnan and Hainan,and Tanggula Town of Geermu City,a total of 85 human plague episodes were occurred,resulting 238 onsets,134 deaths,and a matality rate of 56.30%.The sources of infection were respectively Himalayan mormot 27.31%(65/238),artiodactyls 14.71%(32/238),carnivora 2.10%(5/238),Lagomorpha 0.42%(1/238),the pneumonic plague patient 49.16%(117/238),and biting of flea 6.30%(15/238).The prevalent season was from May all the way to November,the peak-months were August and September.After October,the sheep as the source of infection initiating human being plague accounted for 23.53%.Among the clinical types,the most prevalent type was pneumonic type(61.34%),and the rest,glandular type(17.23%),septic type(16.81%)and other types(4.62%),but the first plague case in each epidemic was mainly the glandular plague.Conclusions In recent years,the tendency of human plague prevalence increases in Sanjiangyuan Area,it is urgent to improve and adjust the prevention and treatment measures in time.
10.Observation of protective effect on mice after immunization with Yersinia pestis capsular antigen F1 and recombinant rV270
Rui-xia, DAI ; Zhi-zhen, QI ; Ling-ling, REN ; Qing-wen, ZHANG ; Cun-xiang, LI ; Rong-jie, WEI ; Hai-lian, WU ; Xiao-yi, WANG ; Zu-yun, WANG
Chinese Journal of Endemiology 2011;30(6):646-648
Objective To evaluate the protective effect of Yersinia pestis capsular antigen F1 and recombinant rV270 on mice after immunization with them.Methods According to body weight,40 female Balb/c mice aged 6 to 8 weeks were randomly divided into four experimental groups(Fl-10 μg + aluminum adjuvant,F1-20 μg + aluminum adjuvant,rV-10 μg + aluminum adjuvant,and rV-20 μg + aluminum adjuvant) and a control group,8 in each group.Mice in experimental groups were immunized with the natural antigen F1 and recombinant antigen rV270 adsorbed to 25% aluminum adjuvant and the control group was immunized with the same amount of aluminum adjuvant.Each mouse was immunized at the hind leg muscle with 100 ml immunizing agent,then a booster immunization was done once on the 21st day after the first immunization.The blood of all mice was collected on the 8th week after the first immunization,serum antibody titers were detected by ELISA and the data of antibody titers were analyzed by t test for comparison between groups.At the same time the mice were injected subcutaneously with 2000-fold LD50 of Yersinia pestis virulent strain 141,after 14 days,the protective effect of immunization was analyzed.Results The control group did not produce antibody.Antibody geometric mean titers (GMT) of the F1-10 mg + aluminum adjuvant and F1-20 mg + aluminum adjuvant groups were 1 ∶ 30443.9,and 1 ∶21527.8,respectively,and compared between the two groups,the difference was not statistically significant (t =1.1282,P > 0.05).The GMTs of the rV-10 μg + aluminum adjuvant and rV-20 μg + aluminum adjuvant groups were 1 ∶ 13957.3 and 1 ∶18100.9,respectively,and compared between the two groups,the difference was not statistically significant(t =0.9408,P > 0.05 ).After subcutaneous injection with Yersinia pestis virulent strain 141,all mice died in the control group but all survived in the experimental group.Conclusion The immune activity of natural antigen F1 and recombinant rV270 is high,which can be used as the main component of subunit vaccine in the plague subunit vaccine study.